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Posts Tagged ‘ programming ’

Networks – social and biological – are all the rage, just now. Indeed, a recent entry at Duncan’s QOTD described the “hairball” network representation as the dominant cultural icon in molecular biology. I’ve not had occasion to explore networks “professionally”, but have always been fascinated by both networks and the tools used to analyse them.

Here’s the situation. Web applications, built using a framework (e.g. Rails, Django) are great for fetching data from a database and rendering it. They’re not so great for crunching and charting the data. Conversely, R is great for crunching and charting, but doesn’t make for a great web application. The idea then, is to let

I came across this blog post just now: The Next Big Thing, and of course these words caught my attention: However, for me personally and for most users, both individual and organizational, the much greater cost of software is the time it takes to install it, maintain it, learn it and document it. On

William asks: How can I make a graph that looks like this, “tweet density” style, showing time intervals? He then helpfully describes his input data: a CSV file with headers “time started, time finished, date”. Here’s a simple CSV file, tasks.csv: task,date,start,end task1,2010-03-05,09:00:00,13:00:00 task2,2010-03-06,10:00:00,15:00:00 task3,2010-03-06,11:00:00,18:00:00 task4,2010-03-07,08:00:00,11:00:00 task5,2010-03-08,14:00:00,17:00:00 task6,2010-03-09,12:00:00,16:00:00 task7,2010-03-10,14:00:00,19:00:00 task8,2010-03-11,09:30:00,13:30:00 Read into R, calculate the

I just added a new video to the R repository, and this one comes from the Los Angeles R Meetup. The folks in LA were fortunate enough to have Dirk Eddelbuettel—renowned R expert and StackOverflow super-user—discuss his joint work with Romain François for interfacing C++ and R code using the Rcpp package. For those

The Lapack routine dspsv solves the linear system of equations Ax=b, where A is a symmetric matrix in packed storage format. However, there appear to be no Lapack functions that compute the determinant of such a matrix. We need to compute the determinant, for instance, in order to compute the multivariate normal density function. The

I’ve been vaguely aware of BioMart for a few years. Inexplicably, I’ve only recently started to use it. It’s one of the most useful applications I’ve ever used. The concept is simple. You have a set of identifiers that describe a biological object, such as a gene. These are called filters. They have values –

After reading (most of) “The Scientists and Engineers Guide to Digital Signal Processing” by Steven W. Smith, PhD, I decided to take a second crack at the ECG data. I wrote a set of R functions that implement a windowed (Blackman) sinc low-pass filter. The convolution of filter kernel with the input signal is conducted

A few months back I gave a presentation to the NYC R Meetup. (R is a statistical programming language. If this means nothing to you, feel free to stop reading now.) The presentation was on ggplot2, a popular package for generating graphs of data and statistics. In the talk (which you can see here, including